From 0d7974c376c4b84dd26096ba0c53ed2535afcbc9 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Wed, 5 Sep 2018 11:07:26 +0200
Subject: gnu: libbigwig: Update to 0.4.2.

* gnu/packages/bioinformatics.scm (libbigwig): Update to 0.4.2.
[source]: Fetch from git.
[arguments]: Disable tests; remove build phases "disable-curl-test" and
"create-target-dirs".
[native-inputs]: Add python-2.
---
 gnu/packages/bioinformatics.scm | 33 ++++++++++++---------------------
 1 file changed, 12 insertions(+), 21 deletions(-)

(limited to 'gnu/packages/bioinformatics.scm')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index f60fc4c84c..7f865ae878 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1887,42 +1887,33 @@ other types of unwanted sequence from high-throughput sequencing reads.")
 (define-public libbigwig
   (package
     (name "libbigwig")
-    (version "0.1.4")
+    (version "0.4.2")
     (source (origin
-              (method url-fetch)
-              (uri (string-append "https://github.com/dpryan79/libBigWig/"
-                                  "archive/" version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/dpryan79/libBigWig.git")
+                    (commit version)))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
-                "098rjh35pi4a9q83n8wiwvyzykjqj6l8q189p1xgfw4ghywdlvw1"))))
+                "0h2smg24v5srdcqzrmz2g23cmlp4va465mgx8r2z571sfz8pv454"))))
     (build-system gnu-build-system)
     (arguments
      `(#:test-target "test"
+       #:tests? #f ; tests require access to the web
        #:make-flags
        (list "CC=gcc"
              (string-append "prefix=" (assoc-ref %outputs "out")))
        #:phases
        (modify-phases %standard-phases
-         (delete 'configure)
-         (add-before 'check 'disable-curl-test
-           (lambda _
-             (substitute* "Makefile"
-               (("./test/testRemote.*") ""))
-             #t))
-         ;; This has been fixed with the upstream commit 4ff6959cd8a0, but
-         ;; there has not yet been a release containing this change.
-         (add-before 'install 'create-target-dirs
-           (lambda* (#:key outputs #:allow-other-keys)
-             (let ((out (assoc-ref outputs "out")))
-               (mkdir-p (string-append out "/lib"))
-               (mkdir-p (string-append out "/include"))
-               #t))))))
+         (delete 'configure))))
     (inputs
      `(("zlib" ,zlib)
        ("curl" ,curl)))
     (native-inputs
-     `(("doxygen" ,doxygen)))
+     `(("doxygen" ,doxygen)
+       ;; Need for tests
+       ("python" ,python-2)))
     (home-page "https://github.com/dpryan79/libBigWig")
     (synopsis "C library for handling bigWig files")
     (description
-- 
cgit v1.2.3


From 8afdeb87518f09383d93cf0dc9b86bde237ba561 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Wed, 5 Sep 2018 11:08:25 +0200
Subject: gnu: python-pybigwig: Update to 0.3.12.

* gnu/packages/bioinformatics.scm (python-pybigwig): Update to 0.3.12.
[propagated-inputs]: Add python-numpy.
---
 gnu/packages/bioinformatics.scm | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioinformatics.scm')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 7f865ae878..05d516165e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1924,13 +1924,13 @@ files.")
 (define-public python-pybigwig
   (package
     (name "python-pybigwig")
-    (version "0.2.5")
+    (version "0.3.12")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "pyBigWig" version))
               (sha256
                (base32
-                "0yrpdxg3y0sny25x4w22lv1k47jzccqjmg7j4bp0hywklvp0hg7d"))
+                "00w4kfnm2c5l7wdwr2nj1z5djv8kzgf7h1zhsgv6njff1rwr26g0"))
               (modules '((guix build utils)))
               (snippet
                '(begin
@@ -1946,6 +1946,8 @@ files.")
              (substitute* "setup.py"
                (("libs=\\[") "libs=[\"BigWig\", "))
              #t)))))
+    (propagated-inputs
+     `(("python-numpy" ,python-numpy)))
     (inputs
      `(("libbigwig" ,libbigwig)
        ("zlib" ,zlib)
-- 
cgit v1.2.3


From ce0e762bf926bcd6f126466c3556a820833621ba Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 5 Sep 2018 13:44:42 +0200
Subject: gnu: r-annotationforge: Update to 1.22.2.

* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.22.2.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioinformatics.scm')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 05d516165e..6028311b3c 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -6371,14 +6371,14 @@ exploration of the results.")
 (define-public r-annotationforge
   (package
     (name "r-annotationforge")
-    (version "1.22.0")
+    (version "1.22.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "AnnotationForge" version))
        (sha256
         (base32
-         "12ffj7h95adiya5mzyjxazqn1qgr434ajpabfcyhrj5v83s4vk65"))))
+         "17kmy7nvpyyj6w5jyrjciw87rydmmmc8q6cnwqjv1j7li9bp09gr"))))
     (properties
      `((upstream-name . "AnnotationForge")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From 3c0437561401986d90de358a8d5fae50d6593261 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 5 Sep 2018 13:46:03 +0200
Subject: gnu: r-biocviews: Update to 1.48.3.

* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.48.3.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioinformatics.scm')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 6028311b3c..e900bd6194 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -6957,13 +6957,13 @@ Bioconductor, CRAN, and Github.")
 (define-public r-biocviews
   (package
     (name "r-biocviews")
-    (version "1.48.2")
+    (version "1.48.3")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "biocViews" version))
               (sha256
                (base32
-                "01yiafayl1m5704xdd2cn3zjc78rs10dqyz66lr3qkf6d8w66938"))))
+                "1rxvwikqivsgxjjcazlszy8xgz346lfh5rw4llxw6fz38fjgb0k5"))))
     (properties
      `((upstream-name . "biocViews")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From 5728d9c6c081b7a0eeb6d29ec221d4638f6dd083 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 5 Sep 2018 13:46:20 +0200
Subject: gnu: r-iranges: Update to 2.14.11.

* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.14.11.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioinformatics.scm')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index e900bd6194..5aec3cc6ae 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7176,13 +7176,13 @@ utilities for sequence data management under the ACNUC system.")
 (define-public r-iranges
   (package
     (name "r-iranges")
-    (version "2.14.10")
+    (version "2.14.11")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "IRanges" version))
               (sha256
                (base32
-                "10ccw930vfmkskkrzbps14xglqlkxf588623dr7f1a9ckx7yr2p6"))))
+                "0wz63hysspyjihqadg91dbvllc5a61zzjrsz0b9498lihqc6m1la"))))
     (properties
      `((upstream-name . "IRanges")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From 1adf4596a6d268c3d2a249d235569631f8df306f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 5 Sep 2018 13:48:36 +0200
Subject: gnu: r-edger: Update to 3.22.3.

* gnu/packages/bioinformatics.scm (r-edger): Update to 3.22.3.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioinformatics.scm')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 5aec3cc6ae..b6b6e7267c 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7256,13 +7256,13 @@ names in their natural, rather than lexicographic, order.")
 (define-public r-edger
   (package
     (name "r-edger")
-    (version "3.22.2")
+    (version "3.22.3")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "edgeR" version))
               (sha256
                (base32
-                "07py2g6vg9jbflwhc1hnzr2silbinrjwxq3mkq30nzjgf0n0hrf3"))))
+                "0w3jv29n0kkaiig8dbbdqy2dkng8xfaihch82mj9ci5hphrx3nng"))))
     (properties `((upstream-name . "edgeR")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 33a103a54393f4e8994b2cb46f6be7d8942cc42e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 5 Sep 2018 13:51:48 +0200
Subject: gnu: r-variantannotation: Update to 1.26.1.

* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.26.1.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioinformatics.scm')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b6b6e7267c..6efb6f1c1b 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7284,13 +7284,13 @@ CAGE.")
 (define-public r-variantannotation
   (package
     (name "r-variantannotation")
-    (version "1.26.0")
+    (version "1.26.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "VariantAnnotation" version))
               (sha256
                (base32
-                "06bccdf57vja7m63chmgc4539lwng3q3b8zxn285fj8524l6mcn7"))))
+                "1r55ki951dj81qvy73knfcy69ik5vzkd56wnk3f6vvf9vngqb8jr"))))
     (properties
      `((upstream-name . "VariantAnnotation")))
     (inputs
-- 
cgit v1.2.3


From 688cb0852706d1e2d0cc03c707a04098ab59b98b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 5 Sep 2018 13:52:03 +0200
Subject: gnu: r-limma: Update to 3.36.3.

* gnu/packages/bioinformatics.scm (r-limma): Update to 3.36.3.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioinformatics.scm')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 6efb6f1c1b..29558768c0 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7322,13 +7322,13 @@ coding changes and predict coding outcomes.")
 (define-public r-limma
   (package
     (name "r-limma")
-    (version "3.36.1")
+    (version "3.36.3")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "limma" version))
               (sha256
                (base32
-                "1982g5v35ilfgxm2vkq1p3j1bbir795pjvfzx4nzam2rlqqymbqm"))))
+                "0iiifszr6hcqih6kszdsbkx3gacfg3d7v8hdx0lbjqnjqgqz7pwk"))))
     (build-system r-build-system)
     (home-page "http://bioinf.wehi.edu.au/limma")
     (synopsis "Package for linear models for microarray and RNA-seq data")
-- 
cgit v1.2.3


From 1d56c79f86cd0c776e76a1bece26622f56c28f12 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 5 Sep 2018 13:52:53 +0200
Subject: gnu: r-genomicranges: Update to 1.32.6.

* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.32.6.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioinformatics.scm')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 29558768c0..2b467145d0 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7377,13 +7377,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.")
 (define-public r-genomicranges
   (package
     (name "r-genomicranges")
-    (version "1.32.3")
+    (version "1.32.6")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomicRanges" version))
               (sha256
                (base32
-                "03gmka6rlz18vd4229796l5l3l6446v5cb90sn2nb5knjbp84hni"))))
+                "0p58yk2i5gqvjlkx548mnrr49wvs0xfcl06l9rqj2hi6hkkbvnp3"))))
     (properties
      `((upstream-name . "GenomicRanges")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From a02340058c15a22cf8c942c96d0053b8e0881452 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 5 Sep 2018 13:58:33 +0200
Subject: gnu: r-biocparallel: Update to 1.14.2.

* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.14.2.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioinformatics.scm')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 2b467145d0..9d55198f4f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7488,13 +7488,13 @@ powerful online queries from gene annotation to database mining.")
 (define-public r-biocparallel
   (package
     (name "r-biocparallel")
-    (version "1.14.1")
+    (version "1.14.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BiocParallel" version))
               (sha256
                (base32
-                "00qg1kg2l9qqpyjaw5q910cmf84vwfiw1fhsx3ig784gwinwgj6n"))))
+                "1llb5a62hn4yxpdgqdh2l7i5zd06mjkk8hagsna69cq65wv6iifm"))))
     (properties
      `((upstream-name . "BiocParallel")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From 3e61c2a8b1dfbc03f9506aaf10df57651728a7d8 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 5 Sep 2018 13:58:44 +0200
Subject: gnu: r-rsamtools: Update to 1.32.3.

* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.32.3.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioinformatics.scm')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 9d55198f4f..c682399ace 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7539,13 +7539,13 @@ biological sequences or sets of sequences.")
 (define-public r-rsamtools
   (package
     (name "r-rsamtools")
-    (version "1.32.0")
+    (version "1.32.3")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "Rsamtools" version))
               (sha256
                (base32
-                "1s65y5wn4d0x8zsljg2kmhcl6r9884h95kr041j7hp49bmxg3an6"))))
+                "1hpjr22h33pf4fgv0sj83rqzv6l5l7s6fpmmqvchh45ikks1mnhq"))))
     (properties
      `((upstream-name . "Rsamtools")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From aea1b6fb8a9b48b35139e146faffaf27463091b8 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 5 Sep 2018 13:59:06 +0200
Subject: gnu: r-delayedarray: Update to 0.6.5.

* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.6.5.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioinformatics.scm')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index c682399ace..d9d70ea97b 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7583,13 +7583,13 @@ files.")
 (define-public r-delayedarray
   (package
     (name "r-delayedarray")
-    (version "0.6.1")
+    (version "0.6.5")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "DelayedArray" version))
               (sha256
                (base32
-                "0sjwszxdi0vkj2i2di5i46gh9chc660yr3gs5nk9qnqp77713zds"))))
+                "10b03zrnvz5isfh4z55hasya2m71lrfx10l5lm2sdmqs0gwkanrd"))))
     (properties
      `((upstream-name . "DelayedArray")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From f2e79823c697843afd880e79e7f810ad69411722 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 5 Sep 2018 13:59:25 +0200
Subject: gnu: r-rtracklayer: Update to 1.40.6.

* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.40.6.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioinformatics.scm')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index d9d70ea97b..3610f823dc 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7678,13 +7678,13 @@ alignments.")
 (define-public r-rtracklayer
   (package
     (name "r-rtracklayer")
-    (version "1.40.3")
+    (version "1.40.6")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "rtracklayer" version))
               (sha256
                (base32
-                "0kvsjdaypn1jnxbnsxpycildwdyxwnjkigfq8qm8mlyfc4ahdgy3"))))
+                "1wxxxlyps19dw3i0pw4mlm3kinnswsc35rgvlnbwvpnpjbca6w4l"))))
     (build-system r-build-system)
     (arguments
      `(#:phases
-- 
cgit v1.2.3


From ad2ed8d01fa3a5486072f0f484beb74129928796 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 5 Sep 2018 13:59:44 +0200
Subject: gnu: r-genomicfeatures: Update to 1.32.2.

* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.32.2.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioinformatics.scm')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 3610f823dc..0631d59651 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7725,13 +7725,13 @@ as well as query and modify the browser state, such as the current viewport.")
 (define-public r-genomicfeatures
   (package
     (name "r-genomicfeatures")
-    (version "1.32.0")
+    (version "1.32.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomicFeatures" version))
               (sha256
                (base32
-                "1cqcl72q0k5wylw1brn4g4h7xzys1v06piry19cvp0gjcvm5sp7a"))))
+                "0kfyyg1ib8fkq2hxraal10z4bx3rg8figdskw4yhn1mbh6l42q5f"))))
     (properties
      `((upstream-name . "GenomicFeatures")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From 48b21f8b6b7fcd6d0857fc1ac75dddb52bbabdf4 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 5 Sep 2018 14:00:00 +0200
Subject: gnu: r-seqminer: Update to 6.1.

* gnu/packages/bioinformatics.scm (r-seqminer): Update to 6.1.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioinformatics.scm')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 0631d59651..878f5723da 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9321,14 +9321,14 @@ unmodeled, or latent sources of noise.")
 (define-public r-seqminer
   (package
     (name "r-seqminer")
-    (version "6.0")
+    (version "6.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "seqminer" version))
        (sha256
         (base32
-         "057j1l6dip35l1aivilapl2zv9db677b3di2pb3sfgq2sxg0ps3l"))))
+         "15yhg4vfc7jg1jnqb3371j00pgbmbyc9l1xx63hq1l3p34lazq2l"))))
     (build-system r-build-system)
     (inputs
      `(("zlib" ,zlib)))
-- 
cgit v1.2.3


From 4ee8c37cca305dd7c581a7bf0fcf82fa351104a8 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 5 Sep 2018 14:00:56 +0200
Subject: gnu: r-maldiquant: Update to 1.18.

* gnu/packages/bioinformatics.scm (r-maldiquant): Update to 1.18.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioinformatics.scm')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 878f5723da..5b8a1a23b0 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9375,14 +9375,14 @@ trait.")
 (define-public r-maldiquant
   (package
     (name "r-maldiquant")
-    (version "1.17")
+    (version "1.18")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "MALDIquant" version))
        (sha256
         (base32
-         "047s6007ydc38x8wm027mlb4mngz15n0d4238fr8h43wyll5zy0z"))))
+         "18nl214xjsxkcpbg79jkmw0yznwm5szyh2qb84n7ip46mm779ha6"))))
     (properties `((upstream-name . "MALDIquant")))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/MALDIquant")
-- 
cgit v1.2.3


From 07bd90ce90784eb6803c581a18d8b335ce49e1bd Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 5 Sep 2018 14:01:19 +0200
Subject: gnu: r-msnbase: Update to 2.6.3.

* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.6.3.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioinformatics.scm')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 5b8a1a23b0..01603d2937 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9619,14 +9619,14 @@ structure (pcaRes) to provide a common interface to the PCA results.")
 (define-public r-msnbase
   (package
     (name "r-msnbase")
-    (version "2.6.1")
+    (version "2.6.3")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MSnbase" version))
        (sha256
         (base32
-         "0zrpx9r93q5ca2zdak5rs2m9sjm0wjdra1xfj3d3sx6p5gzfyg6n"))))
+         "15jhqg02ypmznc0wxksw56yij02csy678vqy531fdv86fsmypwa0"))))
     (properties `((upstream-name . "MSnbase")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 6f6aef80e3def1ffa7c8e4b0f75b22bd2ececc74 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 5 Sep 2018 14:20:56 +0200
Subject: gnu: r-seurat: Update to 2.3.4.

* gnu/packages/bioinformatics.scm (r-seurat): Update to 2.3.4.
[source]: Remove snippet.
[arguments]: Remove.
[native-inputs]: Remove.
[propagated-inputs]: Remove r-caret, r-diffusionmap, r-fnn, r-gdata, r-ranger,
r-stringr, r-tclust, and rvgam; add r-httr.
---
 gnu/packages/bioinformatics.scm | 39 ++++-----------------------------------
 1 file changed, 4 insertions(+), 35 deletions(-)

(limited to 'gnu/packages/bioinformatics.scm')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 01603d2937..c29122b0cf 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9701,58 +9701,31 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.")
 (define-public r-seurat
   (package
     (name "r-seurat")
-    (version "2.3.2")
+    (version "2.3.4")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "Seurat" version))
               (sha256
                (base32
-                "1sjpy5rrpvlpm6hs7qy7qpglgbp7zrgfybcsalpmjb51rhxhgcg1"))
-              ;; Delete pre-built jar.
-              (snippet
-               '(begin (delete-file "inst/java/ModularityOptimizer.jar")
-                       #t))))
+                "0l8bv4i9nzz26mirnva10mq6pimibj24vk7vpvfypgn7xk4942hd"))))
     (properties `((upstream-name . "Seurat")))
     (build-system r-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'build-jar
-           (lambda* (#:key inputs #:allow-other-keys)
-             (let ((classesdir "tmp-classes"))
-               (setenv "JAVA_HOME" (assoc-ref inputs "jdk"))
-               (mkdir classesdir)
-               (with-output-to-file "manifest"
-                 (lambda _
-                   (display "Manifest-Version: 1.0
-Main-Class: ModularityOptimizer\n")))
-               (and (zero? (apply system* `("javac" "-d" ,classesdir
-                                            ,@(find-files "java" "\\.java$"))))
-                    (zero? (system* "jar"
-                                    "-cmf" "manifest"
-                                    "inst/java/ModularityOptimizer.jar"
-                                    "-C" classesdir  ".")))))))))
-    (native-inputs
-     `(("jdk" ,icedtea "jdk")))
     (propagated-inputs
      `(("r-ape" ,r-ape)
-       ("r-caret" ,r-caret)
        ("r-cluster" ,r-cluster)
        ("r-cowplot" ,r-cowplot)
-       ("r-diffusionmap" ,r-diffusionmap)
        ("r-dosnow" ,r-dosnow)
        ("r-dplyr" ,r-dplyr)
        ("r-dtw" ,r-dtw)
        ("r-fitdistrplus" ,r-fitdistrplus)
-       ("r-fnn" ,r-fnn)
        ("r-foreach" ,r-foreach)
        ("r-fpc" ,r-fpc)
-       ("r-gdata" ,r-gdata)
        ("r-ggplot2" ,r-ggplot2)
        ("r-ggridges" ,r-ggridges)
        ("r-gplots" ,r-gplots)
        ("r-hdf5r" ,r-hdf5r)
        ("r-hmisc" ,r-hmisc)
+       ("r-httr" ,r-httr)
        ("r-ica" ,r-ica)
        ("r-igraph" ,r-igraph)
        ("r-irlba" ,r-irlba)
@@ -9765,7 +9738,6 @@ Main-Class: ModularityOptimizer\n")))
        ("r-pbapply" ,r-pbapply)
        ("r-plotly" ,r-plotly)
        ("r-png" ,r-png)
-       ("r-ranger" ,r-ranger)
        ("r-rann" ,r-rann)
        ("r-rcolorbrewer" ,r-rcolorbrewer)
        ("r-rcpp" ,r-rcpp)
@@ -9776,11 +9748,8 @@ Main-Class: ModularityOptimizer\n")))
        ("r-rocr" ,r-rocr)
        ("r-rtsne" ,r-rtsne)
        ("r-sdmtools" ,r-sdmtools)
-       ("r-stringr" ,r-stringr)
-       ("r-tclust" ,r-tclust)
        ("r-tidyr" ,r-tidyr)
-       ("r-tsne" ,r-tsne)
-       ("r-vgam" ,r-vgam)))
+       ("r-tsne" ,r-tsne)))
     (home-page "http://www.satijalab.org/seurat")
     (synopsis "Seurat is an R toolkit for single cell genomics")
     (description
-- 
cgit v1.2.3


From 3c553046888943842d953012759aacde255c4e0c Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 5 Sep 2018 14:27:26 +0200
Subject: gnu: r-edaseq: Update to 2.14.1.

* gnu/packages/bioinformatics.scm (r-edaseq): Update to 2.14.1.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioinformatics.scm')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index c29122b0cf..0860d85bab 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9822,14 +9822,14 @@ distribution.")
 (define-public r-edaseq
   (package
     (name "r-edaseq")
-    (version "2.14.0")
+    (version "2.14.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "EDASeq" version))
        (sha256
         (base32
-         "1832pb3jkim4vrqzb8lajwx9r482bhww5n9nz3s6crvyamlp2dj0"))))
+         "0970w9d5ddqw1qxqqafdidkxh6hmcv9j5djwgnpz3fgl05kmysg8"))))
     (properties `((upstream-name . "EDASeq")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From ff7c7d62f464d0a8d5e91ef058579ad03247d817 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 5 Sep 2018 14:29:51 +0200
Subject: gnu: r-keggrest: Update to 1.20.1.

* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.20.1.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioinformatics.scm')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 0860d85bab..eb7d2b840a 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9949,14 +9949,14 @@ microarrays or GRanges for sequencing data.")
 (define-public r-keggrest
   (package
     (name "r-keggrest")
-    (version "1.20.0")
+    (version "1.20.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "KEGGREST" version))
        (sha256
         (base32
-         "1349vidgl9m10l1rbrp3pkwwgi2xcbsw9h9z2xqbvg97lmqc4r8j"))))
+         "1ss0xd5570x570v01r6lp64rr1apjrzp0j62520pvm3g8knjhfvs"))))
     (properties `((upstream-name . "KEGGREST")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 70daf9362b328079886ed7854e6afe4d96181323 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 5 Sep 2018 14:30:16 +0200
Subject: gnu: r-biovizbase: Update to 1.28.2.

* gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.28.2.
[propagated-inputs]: Add r-rlang.
---
 gnu/packages/bioinformatics.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioinformatics.scm')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index eb7d2b840a..f65dad5f96 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10169,14 +10169,14 @@ the fact that each of these packages implements a select methods.")
 (define-public r-biovizbase
   (package
     (name "r-biovizbase")
-    (version "1.28.0")
+    (version "1.28.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biovizBase" version))
        (sha256
         (base32
-         "0lkiqdr3ics6hgv47lwkykcy761823bbkhffbn4ykyfzyqwl4p67"))))
+         "0wc45j3hfn01i44bkkxjj3n8b8xzbkkcdv35mrkzb1f9yprkf8gq"))))
     (properties `((upstream-name . "biovizBase")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10193,6 +10193,7 @@ the fact that each of these packages implements a select methods.")
        ("r-hmisc" ,r-hmisc)
        ("r-iranges" ,r-iranges)
        ("r-rcolorbrewer" ,r-rcolorbrewer)
+       ("r-rlang" ,r-rlang)
        ("r-rsamtools" ,r-rsamtools)
        ("r-s4vectors" ,r-s4vectors)
        ("r-scales" ,r-scales)
-- 
cgit v1.2.3


From 16527f1cbc8af73b1034ddce2edf9e2bce094564 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 5 Sep 2018 14:31:06 +0200
Subject: gnu: r-ggbio: Update to 1.28.5.

* gnu/packages/bioinformatics.scm (r-ggbio): Update to 1.28.5.
[propagated-inputs]: Add r-rlang.
---
 gnu/packages/bioinformatics.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioinformatics.scm')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index f65dad5f96..9882356a08 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10211,14 +10211,14 @@ effort and encourages consistency.")
 (define-public r-ggbio
   (package
     (name "r-ggbio")
-    (version "1.28.0")
+    (version "1.28.5")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ggbio" version))
        (sha256
         (base32
-         "0wszh3w8yia5zw758h837i1q35k99sn444y2hahcxqbdmmlbf7in"))))
+         "19s2v40fycwf44fl3lm791y635xzw67b30sq2g0qq4a6phjik42d"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)
@@ -10241,6 +10241,7 @@ effort and encourages consistency.")
        ("r-iranges" ,r-iranges)
        ("r-organismdbi" ,r-organismdbi)
        ("r-reshape2" ,r-reshape2)
+       ("r-rlang" ,r-rlang)
        ("r-rsamtools" ,r-rsamtools)
        ("r-rtracklayer" ,r-rtracklayer)
        ("r-s4vectors" ,r-s4vectors)
-- 
cgit v1.2.3


From e69c07e61a870861f5c9d9f114e2783cba213934 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 5 Sep 2018 14:32:25 +0200
Subject: gnu: r-hdf5array: Update to 1.8.1.

* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.8.1.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioinformatics.scm')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 9882356a08..53bf86180f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10696,14 +10696,14 @@ problems in genomics, brain imaging, astrophysics, and data mining.")
 (define-public r-hdf5array
   (package
     (name "r-hdf5array")
-    (version "1.8.0")
+    (version "1.8.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "HDF5Array" version))
        (sha256
         (base32
-         "1l0276qxkhgdxsfck3jmi8jvnsr20g10gjki53g0mqa45wnhm3ck"))))
+         "1s44zgm9jg82bk4b8k3dh7xw7mxychlfm3grs8516mxnw91zpvy5"))))
     (properties `((upstream-name . "HDF5Array")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 8e44ff0c0de2ee752ccaf9189d882735d3185c65 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 5 Sep 2018 14:37:02 +0200
Subject: gnu: r-scater: Update to 1.8.4.

* gnu/packages/bioinformatics.scm (r-scater): Update to 1.8.4.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioinformatics.scm')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 53bf86180f..687cb131d2 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10842,13 +10842,13 @@ libraries.")
 (define-public r-scater
   (package
     (name "r-scater")
-    (version "1.8.0")
+    (version "1.8.4")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "scater" version))
               (sha256
                (base32
-                "0bhpikgz3b9f510dawsay4zry9rlp8vjx5n6zvwbcpwrd94p3903"))))
+                "173lfpas2fqsp4xxsw01wkxd4496c5p8himw9b4r9z4npxkfyv16"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-beachmat" ,r-beachmat)
-- 
cgit v1.2.3


From f0771741781ff75af42ea59027a592ac159bcf98 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 5 Sep 2018 14:41:37 +0200
Subject: gnu: r-scran: Update to 1.8.4.

* gnu/packages/bioinformatics.scm (r-scran): Update to 1.8.4.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioinformatics.scm')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 687cb131d2..760b716408 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10886,14 +10886,14 @@ quality control.")
 (define-public r-scran
   (package
     (name "r-scran")
-    (version "1.8.2")
+    (version "1.8.4")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "scran" version))
        (sha256
         (base32
-         "0nbn5x75gf9d0p18w7vpkbv30cpdqvp5bz8xvila0h7jla7xdyih"))))
+         "17vq9vb9ak7n4mcqpwnm9x3z91vmr7xnsgj8f45b8dbj7m0v126j"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-beachmat" ,r-beachmat)
-- 
cgit v1.2.3


From 5dfe491290b14a1ee7efd70f9cd083969c24e1c2 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 5 Sep 2018 19:46:12 +0200
Subject: gnu: r-graph: Move from bioinformatics to bioconductor.

* gnu/packages/bioinformatics.scm (r-graph): Move from here...
* gnu/packages/bioconductor.scm (r-graph): ...to here.
---
 gnu/packages/bioinformatics.scm | 19 -------------------
 1 file changed, 19 deletions(-)

(limited to 'gnu/packages/bioinformatics.scm')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 760b716408..a03d37c5b0 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7787,25 +7787,6 @@ extracting the desired features in a convenient format.")
 information about the latest version of the Gene Ontologies.")
     (license license:artistic2.0)))
 
-(define-public r-graph
-  (package
-    (name "r-graph")
-    (version "1.58.0")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "graph" version))
-              (sha256
-               (base32
-                "1zx445lk36g1s6i5dbhhf00nzzazyklfjxxjfax6q8hnhvgm9759"))))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)))
-    (home-page "https://bioconductor.org/packages/graph")
-    (synopsis "Handle graph data structures in R")
-    (description
-     "This package implements some simple graph handling capabilities for R.")
-    (license license:artistic2.0)))
-
 (define-public r-topgo
   (package
     (name "r-topgo")
-- 
cgit v1.2.3


From dff5640a59da533fc91fa285b6d7d7fec2f7e60a Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 5 Sep 2018 19:55:00 +0200
Subject: gnu: r-rcas: Use standard version of ghc-pandoc-citeproc.

* gnu/packages/bioinformatics.scm (r-rcas)[native-inputs]: Replace
"ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc".
---
 gnu/packages/bioinformatics.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'gnu/packages/bioinformatics.scm')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index a03d37c5b0..028643aeb4 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8518,7 +8518,7 @@ paired-end data.")
      `(("r-testthat" ,r-testthat)
        ;; During vignette building knitr checks that "pandoc-citeproc"
        ;; is in the PATH.
-       ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc-with-pandoc-1)))
+       ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc)))
     (propagated-inputs
      `(("r-biocgenerics" ,r-biocgenerics)
        ("r-biomart" ,r-biomart)
-- 
cgit v1.2.3


From ca248f1db90c2e7b01d734aaa51d330a29fe0937 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 5 Sep 2018 19:55:56 +0200
Subject: gnu: pigx-rnaseq: Use latest version of Pandoc.

* gnu/packages/bioinformatics.scm (pigx-rnaseq)[inputs]: Replace
"ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc", and
"ghc-pandoc-1" with "ghc-pandoc".
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioinformatics.scm')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 028643aeb4..99313824e9 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -12830,8 +12830,8 @@ once.  This package provides tools to perform Drop-seq analyses.")
        ("r-rtracklayer" ,r-rtracklayer)
        ("r-rjson" ,r-rjson)
        ("salmon" ,salmon)
-       ("ghc-pandoc" ,ghc-pandoc-1)
-       ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc-with-pandoc-1)
+       ("ghc-pandoc" ,ghc-pandoc)
+       ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc)
        ("python-wrapper" ,python-wrapper)
        ("python-pyyaml" ,python-pyyaml)))
     (home-page "http://bioinformatics.mdc-berlin.de/pigx/")
-- 
cgit v1.2.3


From 7cd40c8c5dee1b323117ec85787566505be2d9ad Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 5 Sep 2018 19:56:38 +0200
Subject: gnu: pigx-chipseq: Use latest version of Pandoc.

* gnu/packages/bioinformatics.scm (pigx-chipseq)[inputs]: Replace
"ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc", and
"ghc-pandoc-1" with "ghc-pandoc".
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioinformatics.scm')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 99313824e9..e1d953561b 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -12892,8 +12892,8 @@ expression report comparing samples in an easily configurable manner.")
        ("macs" ,macs)
        ("multiqc" ,multiqc)
        ("perl" ,perl)
-       ("ghc-pandoc" ,ghc-pandoc-1)
-       ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc-with-pandoc-1)
+       ("ghc-pandoc" ,ghc-pandoc)
+       ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc)
        ("fastqc" ,fastqc)
        ("bowtie" ,bowtie)
        ("idr" ,idr)
-- 
cgit v1.2.3


From c2b4f81e51bab9a3ca6f2d1ba81ab1ff3b573ab4 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 5 Sep 2018 19:56:53 +0200
Subject: gnu: pigx-bsseq: Use latest version of Pandoc.

* gnu/packages/bioinformatics.scm (pigx-bsseq)[inputs]: Replace
"ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc", and
"ghc-pandoc-1" with "ghc-pandoc".
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioinformatics.scm')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index e1d953561b..7c25a71c6b 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -12954,8 +12954,8 @@ in an easily configurable manner.")
        ("r-bookdown" ,r-bookdown)
        ("r-ggplot2" ,r-ggplot2)
        ("r-ggbio" ,r-ggbio)
-       ("ghc-pandoc" ,ghc-pandoc-1)
-       ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc-with-pandoc-1)
+       ("ghc-pandoc" ,ghc-pandoc)
+       ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc)
        ("python-wrapper" ,python-wrapper)
        ("python-pyyaml" ,python-pyyaml)
        ("snakemake" ,snakemake-4)
-- 
cgit v1.2.3


From 00a43cb81cecb30d40f9940407c9f1ba08d3d38e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 5 Sep 2018 19:57:09 +0200
Subject: gnu: pigx-scrnaseq: Use latest version of Pandoc.

* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Replace
"ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc", and
"ghc-pandoc-1" with "ghc-pandoc".
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioinformatics.scm')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 7c25a71c6b..92b6e7d50c 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -13005,8 +13005,8 @@ methylation and segmentation.")
        ("python-magic" ,python-magic)
        ("python-numpy" ,python-numpy)
        ("python-loompy" ,python-loompy)
-       ("ghc-pandoc" ,ghc-pandoc-1)
-       ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc-with-pandoc-1)
+       ("ghc-pandoc" ,ghc-pandoc)
+       ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc)
        ("samtools" ,samtools)
        ("snakemake" ,snakemake-4)
        ("star" ,star)
-- 
cgit v1.2.3


From d53aeeafccb91fd03c6c540153720717eceb92a4 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 6 Sep 2018 04:53:32 +0200
Subject: Add missing use-modules clause.

This is a follow-up to commit 5dfe491290b14a1ee7efd70f9cd083969c24e1c2.
Sorry!

* gnu/packages/bioinformatics.scm, gnu/packages/graph.scm: Use (gnu packages
bioconductor).
---
 gnu/packages/bioinformatics.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu/packages/bioinformatics.scm')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 92b6e7d50c..2d5ec6d170 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -51,6 +51,7 @@
   #:use-module (gnu packages base)
   #:use-module (gnu packages bash)
   #:use-module (gnu packages bison)
+  #:use-module (gnu packages bioconductor)
   #:use-module (gnu packages boost)
   #:use-module (gnu packages check)
   #:use-module (gnu packages compression)
-- 
cgit v1.2.3